Optimum geometries and relative energies for cytosine,thymine, uracil,the imino tautomer of cytosine,the enol tautomer of thymine,and the enol tautomer of uracil by the MINDO/2 SCF MO method

A MINDO /2 SCF MO geometry optimization of cytosine (C), thymine (T), uracil (U), the imino tautomer of cytosine (C*), the enol tautomer of thymine (T*), and the enol tautomer of uracil (U*)was made. The optimized geometries for cytosine, thymine, and uracil agree well with crystallographic data. The optimized geometries for the tautomers show the correct trends in bond lengthening and bond angle except for the C4—O4 length and C4—O4—H angle of T* and U*. The energies of tautomerization were found to be 10.3, ?9.0, and ?14.2 kcal/mol for C?C*, T?T*, and U?U*, respectively, when optimized geometries are used. The overestimation of the C4—O4—H angle is speculated to arise because of an inadequacy in the parametrization of the one-center integrals in MINDO /2.     

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

Nonradiative deactivation mechanisms of uracil, thymine, and 5-fluorouracil: a comparative ab initio study

The mechanisms of the ultrafast nonradiative deactivation of uracil and its substituted derivatives thymine (5-methyluracil) and 5-fluorouracil after absorption of UV light are explored and compared by means of ab initio multistate (MS) CASPT2 calculations. The MS-CASPT2 method is applied for the calculation of potential energy profiles, especially for the geometry optimization in the electronically excited state, with the aim of an accurate prediction of deactivation pathways. The resulting energy curves of each molecule exhibit that the conical intersection between the (1)ππ* and ground states is accessible via small energy barriers from the minimum in the (1)ππ* state as well as from that in the (1)nπ* state. The barrier of 5-fluorouracil in the (1)ππ* state is calculated to be definitely higher than those of uracil and thymine, which is consistent with experiments and suggests that the elongation of the excited-state lifetime of uracil by fluorine substitution is significantly contributed from intrinsic electronic effect of the molecule. However, no evidence of the experimentally observed longer excited-state lifetime of thymine than uracil is found in the presently calculated MS-CASPT2 potential energy curves in the (1)ππ* and (1)nπ* states, implying nonnegligible contribution of other factors such as solvation effect and substituent mass to the photoinduced dynamics of uracil derivatives.     

Nonconventional hydrogen bonds: a theoretical study of [uracil-L](-) (L = F, Cl, Br, I, Al, Ga, In) complexes

The interaction of L (-) (L = F, Cl, Br, I, Al, Ga and In) with a uracil molecule has been studied with B3LYP density-functional geometry optimizations and electron-propagator calculations of vertical electron detachment energies. Because the extra electron of the anion is localized on L, nonconventional hydrogen bonds are formed. The interactions of halide anions with uracil are similar to the interactions of uracil with Cu (-), Ag (-) and Au (-) that were reported previously. Whereas halide and transition metal anion complexes with uracils are singlets, the anions formed with Al, Ga and In are triplets. Vertical electron detachment energies (VEDEs) are higher for (uracil-L) (-) than the analogous values for isolated L (-) anions. Predicted VEDEs are assigned to Dyson orbitals that may be localized on L (-) or uracil.     

Homopairing possibilities of the DNA base thymine and the RNA base uracil: an ab initio density functional theory study

All planar homopairings of the DNA base thymine and the RNA base uracil are reported for the first time in this study. Using the idea of binding sites discussed in our previous work (Kelly et al. J. Phys. Chem. B 2005, 109, 11933; J. Phys. Chem. B 2005, 109, 22045) and ab initio density functional theory, we predict and relax 10 thymine and 10 uracil homopairs. The stabilization energies of the homopairs vary from just below zero to -0.82 eV. The results on the pair geometry and energetics are compared with those available in the literature. The collected data on all planar thymine and uracil homopairs can be used to construct the thymine and uracil superstructures seen experimentally on various surfaces.     

Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives

The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.     

A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil

Molecular geometries of the nucleic acid bases thymine, cytosine and uracil in the ground and the lowest two singlet excited states were optimized using the ab initio approach employing the 4-31G basis set for all the atoms except the amino group of cytosine for which the 6-311+G^* basis set was used. The excited state calculations were performed employing configuration interaction involving singly excited configurations (CIS). Vibrational frequencies were computed in order to examine the nature of the stationary points on the potential energy surfaces obtained by geometry optimization. While the ground state geometries of uracil and thymine (except the methyl group hydrogens) are planar, the corresponding excited state geometries were found to be significantly nonplanar. In the case of cytosine, the amino group is pyramidal and the rest of the molecule is only slightly nonplanar in the ground state, but the excited state geometries are appreciably nonplanar. In particular, consequent to the S₂(n–π^*) excitation of cytosine, the amino group plane is strongly rotated. While thymine is stable in the S₂(π–π^*) excited state, uracil appears to be dissociative in the corresponding excited state.     

The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry

We present M06-2X density functional calculations of the chloroform/water partition coefficients of cytosine, thymine, uracil, adenine, and guanine and calculations of the free energies of association of selected unsubstituted and alkylated nucleotide base pairs in chloroform and water. Both hydrogen bonding and π-π stacking interactions are considered. Solvation effects are treated using the continuum solvent models SM8, SM8AD, and SMD, including geometry optimization in solution. Comparison of theoretical results with available experimental data indicates that all three of these solvation models predict the chloroform-water partition coefficients for the studied nucleobases qualitatively well, with mean unsigned errors in the range of 0.4-1.3 log units. All three models correctly predict the preference for hydrogen bonding over stacking for nucleobase pairs solvated in chloroform, and SM8, SM8AD, and SMD show similar accuracy in predicting the corresponding free energies of association. The agreement between theory and experiment for the association free energies of the dimers in water is more difficult to assess, as the relevant experimental data are indirect. Theory predicts that the stacking interaction of nucleobases in water is more favorable than hydrogen bonding for only two out of three tested hetero-dimers.     

Radiation damage of biosystems mediated by secondary electrons: resonant precursors for uracil molecules

Calculations are presented for the energy locations and spatial structures of low-energy resonant states describing transient negative ions (TNIs) of the uracil molecule in the gas phase. The resonant states are modeled using scattering calculations of low energy electrons interacting with isolated molecules in their equilibrium geometry. The interaction forces used in this model are described in detail. Examination of the spatial densities of the excess resonant electrons for the various TNIs found by the calculations allows one to associate the metastable anions with specific features of the experimentally observed fragmentation patterns.     

Effects of microsolvation on uracil and its radical anion: uracil(H2O)n (n = 1-5)

Microsolvation effects on the stabilities of uracil and its anion have been investigated by explicitly considering the structures of complexes of uracil with up to five water molecules at the B3LYPDZP++ level of theory. For all five systems, the global minimum of the neutral cluster has a different equilibrium geometry from that of the radical anion. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of uracil are predicted to increase gradually with the number of hydrating molecules, qualitatively consistent with experimental results from a photodetachment-photoelectron spectroscopy study [J. Schiedt et al., Chem. Phys. 239, 511 (1998)]. The trend in the AEAs implies that while the conventional valence radical anion of uracil is only marginally bound in the gas phase, it will form a stable anion in aqueous solution. The gas-phase AEA of uracil (0.24 eV) was higher than that of thymine by 0.04 eV and this gap was not significantly affected by microsolvation. The largest AEA is that predicted for uracil(H2O)5, namely, 0.96 eV. The VDEs range from 0.76 to 1.78 eV.     

Geometry,electronic structure and energy barriers of all possible isomers of Fe<Subscript>2</Subscript>C<Subscript>3</Subscript> nanoparticle

The search for stable structures of neutral Fe₂C₃ particle was based on the geometry optimization of the known FeC₃ and Fe₂C₂ isomers with the Fe and C atoms approaching from various directions. The geometry optimization of more than 2,000 initial structures was carried out using the DFT based DMol³ method and converged to 41 stable configurations. The structures containing C₃ triangle and the cyclic planar isomer with transannular bonds are found to have the lowest binding energies. The effective charges and total spin densities on the atoms were calculated using integral scheme incorporated in DVM and Hirshfeld procedure of DMol³. The relations between geometrical structures and spin moments ordering are discussed. For the evaluation of potential barriers the geometry optimization of all Fe₂C₃ configurations was performed with a thermal occupation, corresponding to the various values of the excitation energy.     

Solvation Structure of Uracil in Ionic Liquids

The local solvation environment of uracil dissolved in the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate has been studied using neutron diffraction techniques. At solvent:solute (ionic liquid:uracil) ratios of 3:1 and 2:1, little perturbation of the ion–ion correlations compared to those of the neat ionic liquid are observed. We find that solvation of the uracil is driven predominantly by the acetate anion of the solvent. While short distance correlations exist between uracil and the imidazolium cation, the geometry of these contacts suggest that they cannot be considered as hydrogen bonds, in contrast to other studies by Araújo et al. (J. M. Araújo, A. B. Pereiro, J. N. Canongia‐Lopes, L. P. Rebelo, I. M. Marrucho, J. Phys. Chem. B 2013, 117, 4109–4120 ). Nevertheless, this combination of interactions of the solute with both the cation and anion components of the solvents helps explain the high solubility of the nucleobase in this media. In addition, favourable uracil–uracil contacts are observed, of similar magnitude to those between cation and uracil, and are also likely to aid dissolution.     

Application of chromium‐doped fullerene as a carrier for thymine and uracil nucleotides: Comprehensive density functional theory calculations

The interactions of the nucleobases thymine (C₅H₆N₂O₂) and uracil (C₄H₄N₂O₂) with Cr‐doped C₂₀ fullerene (C₁₉Cr) are investigated by performing density functional theory calculations. The adsorption of these nucleobases on C₁₉Cr leads to two distinct geometries (P1 and P2) differing in the orientation of the nucleobases. The interaction of the nucleobases with the C₁₉Cr nanocluster is highly exothermic, revealing that they are chemically adsorbed on C₁₉Cr. The results show that the binding energy of the thymine–C₁₉Cr complex is slightly higher than that of the uracil–C₁₉Cr complex. In addition, the P2 geometry is more stable compared to P1 due to the higher binding energy in the former configuration. However, based on the results of natural bond orbital and frontier molecular orbitals analyses, the C₁₉Cr nanocage has higher reactivity with the nucleobases in P1 geometry in comparison with P2 due to the larger charge transfer and orbital hybridization in the former geometry. Moreover, the band gap of the C₁₉Cr nanocage decreases after interaction with the nucleobases, and interestingly the impact is more pronounced for P1 geometry, confirming the higher sensitivity of C₁₉Cr to the nucleobases in P1 geometry. Our findings reveal the promising potential of C₁₉Cr as an organometallic carrier for nucleobases thymine and uracil.     

Assignment of electronic transitions by geometry optimization

Adiabatic excitation energies, excited state geometries, excited state charges, bond orders and dipole moments have been obtained for HCN, CO₂,H₂CO, HFCO, F₂CO, ethylene, trans-butadiene, furan, pyrrole and uracil using the SINDO1 semi-empirical method with configuration interaction. Our results generally agree with those ofab initio calculations and experiment satisfactorily. Geometry optimization is found to mix configurations differing in their allowedness in vertical excitation from the ground state, which in turn helps in the assignment of spectral transitions. TheV excited singlet state of trans-butadiene and various excited states of furan, pyrrole and uracil have been found to be appreciably non-planar. The single and double CC bonds are found to exchange positions due to the lowest triplet and singlet transitions of furan and pyrrole. The first triplet and first singlet transitions of uracil have been found to be of π-π* and π-σ* types respectively in agreement with recent experimental findings. On leave of absence from the Department of Physics, Banaras Hindu University, Varanasi-221005, India     

High‐spin states in tetrahedral X4 clusters (X = H,Li, Na,K)

The high‐spin electronic states for lithium, sodium, and potassium four‐atom clusters were studied. In particular, we performed coupled cluster geometry optimization of the quintet state in tetrahedral geometry. The quintet state of these systems is characterized by having all the valence electron unpaired, giving rise to the so‐called no‐pair bonding. Single‐point full configuration interaction computations on the equilibrium geometries for the various clusters are also presented. The analysis of the valence orbitals in a localized representation confirms the importance of the p atomic orbitals to explain this unusual type of bond. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Electron affinities of small uracil-water complexes: a comparison of benchmark CCSD(T) calculations with DFT

We present benchmark CCSD(T) calculations of the adiabatic electron affinities (AEA) and the vertical detachment energies (VDE) of the uracil molecule interacting with one to three water molecules. Calculations with rather large aug-cc-pVTZ basis set were only tractable when the space of virtual orbitals was reduced to about 60% of the full space employing the OVOS (Optimized Virtual Orbital Space) technique. Because of the microhydration, the valence-bound uracil anion is stabilized leading to gradually more positive values of both AEA and VDE with increasing number of participating water molecules. This agrees with experimental findings. Upon hydration by three water molecules, the electron affinity of uracil increased in comparison with AEA of the isolated molecule by about 250 up to 570 meV, depending on the geometry of the complex. CCSD(T) results confirm trends determined by DFT calculations of the microhydrated uracil and its anion, even if electron affinities of the free and hydrated uracil molecule are overestimated by DFT by up to 300 meV.     

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]+ Complexes (M=Zn,Cu, Ni,Co, Fe,Mn, Cd,Pd , Mg,Ca, Sr,Ba, and Pb): Loss of Uracil versus HNCO

Complexes formed between metal dications, the conjugate base of uracil, and uracil are investigated by sustained off‐resonance irradiation collision‐induced dissociation (SORI‐CID) in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Positive‐ion electrospray spectra show that [M(Ura?H)(Ura)]⁺ (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd, Mg, Ca, Sr, Ba, or Pb) is the most abundant ion even at low concentrations of uracil. SORI‐CID experiments show that the main primary decomposition pathway for all [M(Ura?H)(Ura)]⁺, except where M=Ca, Sr, Ba, or Pb, is the loss of HNCO. Under the same SORI‐CID conditions, when M is Ca, Sr, Ba, or Pb, [M(Ura?H)(Ura)]⁺ are shown to lose a molecule of uracil. Similar results were observed under infrared multiple‐photon dissociation excitation conditions, except that [Ca(Ura?H)(Ura)]⁺ was found to lose HNCO as the primary fragmentation product. The binding energies between neutral uracil and [M(Ura?H)]⁺ (M=Zn, Cu, Ni, Fe, Cd, Pd ,Mg, Ca, Sr Ba, or Pb) are calculated by means of electronic‐structure calculations. The differences in the uracil binding energies between complexes which lose uracil and those which lose HNCO are consistent with the experimentally observed differences in fragmentation pathways. A size dependence in the binding energies suggests that the interaction between uracil and [M(Ura?H)]⁺ is ion–dipole complexation and the experimental evidence presented supports this.     

Synthesis of acyclic and macrocyclic analogs of Di-, Tri-, and tetranucleotides

Compounds consisting of two or three uracil fragments were synthesized by reaction of methyl-substituted uracil sodium salts with 1-(6-bromohexyl)-3,6-dimethyluracil or 1,6-dibromohexane. Treatment of these compounds with paraformaldehyde gave the corresponding pyrimidinophanes and acyclic compounds in which the uracil fragments are linked through methylene bridges. Uracil derivatives having no substituent on N³ were synthesized by reactions of silylated uracils with 1,3-bis(6-bromohexyl)uracil or 4,4′-(6-bromohexyloxy)diphenylmethane. The acyclic compound was converted into pyrimidinophane containing uracil fragments with N³H groups. A trinucleotide analog including uracil and two adenine fragments was synthesized from 1,3-bis(6-bromohexyl)uracil.     

Preparation of organometallic uracil-analogue Fischer carbene complexes: Comparative study of conventional heating vs microwave irradiation

Mono and disubstituted ureas react with alkynyl Fischer carbene complexes to give mono and di N,N-substituted organometallic uracil analogues. An optimization of the process using different starting metal carbene complexes and variously substituted ureas under conventional heating (with and without solvent) and microwave irradiation techniques is reported. The synthesis of the metal-carbene analog of the commercially available dimethyl uracil is reported.     

Geometry optimization of metal complexes using natural internal coordinates: Representation of skeletal degrees of freedom

The geometry optimization using natural internal coordinates was applied for transition metal complexes. The original definitions were extended here for the skeletal degrees of freedom which are related to the translational and rotational displacements of the ηⁿ-bonded ligands. We suggest definitions for skeletal coordinates of ηⁿ-bonded small unsaturated rings and chains. The performance of geometry optimizations using the suggested coordinates were tested on various conformers of 14 complexes. Consideration was given to alternative representations of the skeletal internal coordinates, and the performance of optimization is compared. Using the skeletal internal coordinates presented here, most transition metal complexes were optimized between 10 and 20 geometry optimization cycles in spite of the usually poor starting geometry and crude approximation for the Hessian. We also optimized the geometry of some complexes in Cartesian coordinates using the Hessian from a parametrized redundant force field. We found that it took between two and three times as many iterations to reach convergence in Cartesian coordinates than using natural internal coordinates. © 1997 by John Wiley & Sons, Inc.